[English] 日本語
Yorodumi
- PDB-3q3l: The neutron crystallographic structure of inorganic pyrophosphata... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q3l
TitleThe neutron crystallographic structure of inorganic pyrophosphatase from Thermococcus thioreducens
ComponentsTt-IPPase
KeywordsHYDROLASE / inorganic pyrophosphatase / Neutron / phosphatase / pyrophosphatase
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DEUTERATED WATER / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / REFINEMENT AGAINST FIXED MODEL / Resolution: 2.5 Å
AuthorsHughes, R.C. / Coates, L. / Blakeley, M.P. / Tomanicek, S.J. / Meehan, E.J. / Garcia-Ruiz, J.M. / Ng, J.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.
Authors: Hughes, R.C. / Coates, L. / Blakeley, M.P. / Tomanicek, S.J. / Langan, P. / Kovalevsky, A.Y. / Garcia-Ruiz, J.M. / Ng, J.D.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references / Structure summary
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.4Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tt-IPPase
B: Tt-IPPase
C: Tt-IPPase
D: Tt-IPPase
E: Tt-IPPase
F: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,52612
Polymers125,2856
Non-polymers2406
Water4,288238
1
A: Tt-IPPase
C: Tt-IPPase
E: Tt-IPPase
hetero molecules

A: Tt-IPPase
C: Tt-IPPase
E: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,52612
Polymers125,2856
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area24940 Å2
ΔGint-194 kcal/mol
Surface area34090 Å2
MethodPISA
2
B: Tt-IPPase
D: Tt-IPPase
F: Tt-IPPase
hetero molecules

B: Tt-IPPase
D: Tt-IPPase
F: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,52612
Polymers125,2856
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22450 Å2
ΔGint-188 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.100, 95.510, 113.726
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-179-

DOD

21F-371-

HOH

-
Components

#1: Protein
Tt-IPPase


Mass: 20880.885 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Strain: OGL-20 / Gene: Tt-IPPase / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: H2L2L6*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 298 K / Method: counter diffusion, free-interface diffusion / pH: 6.5
Details: Calcium Chloride, MPD, pH 6.5, counter diffusion, free-interface diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 1 - 2.5
DetectorType: LADI-III / Detector: IMAGE PLATE / Date: Jul 1, 2010
RadiationProtocol: LAUE / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.51
ReflectionResolution: 2.5→37.53 Å / Num. all: 38788 / Num. obs: 28587 / % possible obs: 73.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.146
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.4 / % possible all: 58.7

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
LAUEGENdata collection
LAUEGENdata reduction
LAUESCALEdata scaling
RefinementMethod to determine structure: REFINEMENT AGAINST FIXED MODEL
Starting model: 3I98

3i98


Resolution: 2.5→36.418 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.34 / Isotropic thermal model: isotropic / σ(F): 0.06 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 1425 4.99 %
Rwork0.221 --
obs0.2233 28530 73.13 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.016 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.8628 Å20 Å2-0.7737 Å2
2---6.4316 Å20 Å2
3----7.9679 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 6 238 8812
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.09919128
NEUTRON DIFFRACTIONf_angle_d2.4134600
NEUTRON DIFFRACTIONf_dihedral_angle_d16.3295333
NEUTRON DIFFRACTIONf_chiral_restr0.0761247
NEUTRON DIFFRACTIONf_plane_restr0.0053648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.33651150.31752176NEUTRON DIFFRACTION59
2.5894-2.6930.35041140.28052198NEUTRON DIFFRACTION60
2.693-2.81550.31531210.24742289NEUTRON DIFFRACTION62
2.8155-2.96390.27551250.23482376NEUTRON DIFFRACTION64
2.9639-3.14950.29191320.21652506NEUTRON DIFFRACTION68
3.1495-3.39250.29141420.21992703NEUTRON DIFFRACTION73
3.3925-3.73360.25581530.19082934NEUTRON DIFFRACTION80
3.7336-4.27320.20951680.17613176NEUTRON DIFFRACTION86
4.2732-5.38090.22151760.17893352NEUTRON DIFFRACTION90
5.3809-36.42180.26831790.24533395NEUTRON DIFFRACTION90

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more